chr2-64551540-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_203437.4(AFTPH):c.66T>A(p.Asp22Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000112 in 1,610,008 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_203437.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AFTPH | NM_203437.4 | c.66T>A | p.Asp22Glu | missense_variant | 2/10 | ENST00000409933.6 | NP_982261.2 | |
LOC105374773 | XR_007086343.1 | n.5406-276A>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AFTPH | ENST00000409933.6 | c.66T>A | p.Asp22Glu | missense_variant | 2/10 | 1 | NM_203437.4 | ENSP00000387071 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152090Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250744Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135724
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1457918Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 725392
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152090Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74304
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 19, 2024 | The c.66T>A (p.D22E) alteration is located in exon 2 (coding exon 1) of the AFTPH gene. This alteration results from a T to A substitution at nucleotide position 66, causing the aspartic acid (D) at amino acid position 22 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at